Stupid question but have you connected the ammeter the right way round? If you have the wires wrong on the ammeter it will say -3 amp when in fact its +3 amp. I would connect up a small 12 volt motor or lamp, connect 1 wire to the charging circuit and on to the ground. If you motor or lamp comes on when the engines running, your alternator is working fine and you have the wires on the ammeter the wrong way round. If the motor or lamp doesn't turn on with the engine, You have an alternator problem.
Was the charging circuit working normally before you worked on it?